rs3118590

Positions:

• chr9-134531547-G-A
• chr9-134531547-G-C
• chr9-134531547-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435284.2(ENSG00000228877):​n.103+4263G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,136 control chromosomes in the GnomAD database, including 43,809 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.76 (43809 hom., cov: 32)
• Consequence: ENSG00000228877 ENST00000435284.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506532	NR_188441.1	n.184-13373G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000228877	ENST00000435284.2	n.103+4263G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114934 AN: 152018 Hom.: 43789 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.771

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.756 AC: 115015 AN: 152136 Hom.: 43809 Cov.: 32 AF XY: 0.751 AC XY: 55844 AN XY: 74370

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.772

Alfa AF: 0.734 Hom.: 18947

Bravo AF: 0.773

Asia WGS AF: 0.812 AC: 2822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3118590; hg19: chr9-137423393;